def test_example_distances_calculated_correctly(self):
wall_bounds = ((-2, 4), (-1, 3), (-3, 4))
positions = np.array([[-1., 1, 1], [-2., 1, 1], [-2., 0.5, 1],
[-3., 0.25, 1], [-3, -0.5, 1]])
d_correct = np.array([1, 0, 0, -1, -1])
d = kinematics.distance_from_wall(positions, wall_bounds)
np.testing.assert_array_almost_equal(d, d_correct)
positions = np.array([[0., 0, 0], [1, 0, 5], [1, 0, 0], [0, -2, 0],
[0, -2, -3]])
d_correct = np.array([1., -1, 1, -1, -1])
d = kinematics.distance_from_wall(positions, wall_bounds)
np.testing.assert_array_almost_equal(d, d_correct)
def main():
# loop over all experiments
for expt in session.query(models.Experiment):
print("In experiment '{}'".format(expt.id))
dt = 1 / expt.sampling_frequency
for traj in session.query(
models.Trajectory).filter_by(experiment=expt):
positions = traj.positions(session)
velocities = traj.velocities(session)
# calculate kinematic quantities
velocities_a = kinematics.norm(velocities)
accelerations = kinematics.acceleration(velocities, dt)
accelerations_a = kinematics.norm(accelerations)
headings = kinematics.heading(velocities)
angular_velocities = kinematics.angular_velocity(velocities, dt)
angular_velocities_a = kinematics.norm(angular_velocities)
angular_accelerations = kinematics.acceleration(
angular_velocities, dt)
angular_accelerations_a = kinematics.norm(angular_accelerations)
distance_from_wall = kinematics.distance_from_wall(
positions, WALL_BOUNDS)
# store kinematic quantities in timepoints
for ctr, tp in enumerate(traj.timepoints(session)):
tp.velocity_a = velocities_a[ctr]
tp.acceleration_x, tp.acceleration_y, tp.acceleration_z = accelerations[
ctr]
tp.acceleration_a = accelerations_a[ctr]
tp.heading_xy, tp.heading_xz, tp.heading_xyz = headings[ctr]
tp.angular_velocity_x, tp.angular_velocity_y, tp.angular_velocity_z = angular_velocities[
ctr]
tp.angular_velocity_a = angular_velocities_a[ctr]
tp.angular_acceleration_x, tp.angular_acceleration_y, tp.angular_acceleration_z = angular_accelerations[
ctr]
tp.angular_acceleration_a = angular_accelerations_a[ctr]
tp.distance_from_wall = distance_from_wall[ctr]
session.add(tp)
commit(session)
def test_example_distances_calculated_correctly(self):
wall_bounds = ((-2, 4), (-1, 3), (-3, 4))
positions = np.array([[-1., 1, 1],
[-2., 1, 1],
[-2., 0.5, 1],
[-3., 0.25, 1],
[-3, -0.5, 1]])
d_correct = np.array([1, 0, 0, -1, -1])
d = kinematics.distance_from_wall(positions, wall_bounds)
np.testing.assert_array_almost_equal(d, d_correct)
positions = np.array([[0., 0, 0],
[1, 0, 5],
[1, 0, 0],
[0, -2, 0],
[0, -2, -3]])
d_correct = np.array([1., -1, 1, -1, -1])
d = kinematics.distance_from_wall(positions, wall_bounds)
np.testing.assert_array_almost_equal(d, d_correct)
def main():
# loop over all experiments
for expt in session.query(models.Experiment):
print("In experiment '{}'".format(expt.id))
dt = 1 / expt.sampling_frequency
for traj in session.query(models.Trajectory).filter_by(experiment=expt):
positions = traj.positions(session)
velocities = traj.velocities(session)
# calculate kinematic quantities
velocities_a = kinematics.norm(velocities)
accelerations = kinematics.acceleration(velocities, dt)
accelerations_a = kinematics.norm(accelerations)
headings = kinematics.heading(velocities)
angular_velocities = kinematics.angular_velocity(velocities, dt)
angular_velocities_a = kinematics.norm(angular_velocities)
angular_accelerations = kinematics.acceleration(angular_velocities, dt)
angular_accelerations_a = kinematics.norm(angular_accelerations)
distance_from_wall = kinematics.distance_from_wall(positions, WALL_BOUNDS)
# store kinematic quantities in timepoints
for ctr, tp in enumerate(traj.timepoints(session)):
tp.velocity_a = velocities_a[ctr]
tp.acceleration_x, tp.acceleration_y, tp.acceleration_z = accelerations[ctr]
tp.acceleration_a = accelerations_a[ctr]
tp.heading_xy, tp.heading_xz, tp.heading_xyz = headings[ctr]
tp.angular_velocity_x, tp.angular_velocity_y, tp.angular_velocity_z = angular_velocities[ctr]
tp.angular_velocity_a = angular_velocities_a[ctr]
tp.angular_acceleration_x, tp.angular_acceleration_y, tp.angular_acceleration_z = angular_accelerations[ctr]
tp.angular_acceleration_a = angular_accelerations_a[ctr]
tp.distance_from_wall = distance_from_wall[ctr]
session.add(tp)
commit(session)
